arXiv:2607. 05691v1 Announce Type: cross Abstract: Every chemical language model reading SMILES begins with a tokenizer, yet the field has inherited byte-pair encoding (BPE) from natural language with little scrutiny.
arXiv:2606. 03057v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used for molecular tasks, but it remains unclear which molecular representation to use.
The paper introduces the Latent Core Tokenizer (LCT), a language‑agnostic method that first discovers reusable linguistic units using Minimum Description Length, entropy‑based boundary signals, and morphotactic constraints before building a shared vocabulary. With a 200K‑token vocabulary across 104 languages, LCT shows lower fertility and higher MorphScore than BPE, Unigram, and parity‑aware BPE, while keeping tokenization cost comparable across languages. On four multilingual downstream benchmarks, LCT outperforms the baselines by 1.48, 1.83, and 2.00 aggregate points, demonstrating that compression alone does not guarantee representation quality and underscoring the role of morphology‑driven structural discovery.
The paper audits 22 frontier language models on 12 molecular property regression benchmarks to assess verbatim retrieval of published values. It finds widespread but benchmark‑specific retrieval, with over 50% of models retrieving exact values on five datasets and isolated occurrences on others. Experiments at different reasoning levels show that higher reasoning increases retrieval flags, and attempts to interrupt retrieval reveal that top models can still recognize transformed SMILES and original labels. Suppressing retrieval reduces prediction error variance, indicating that predictive performance is not solely due to memorized values.
arXiv:2608. 03855v1 Announce Type: new Abstract: Transformer models have revolutionized natural language processing (NLP), and text-based molecular representations like SMILES have successfully extended these architectures to chemistry.
arXiv:2606. 12113v1 Announce Type: cross Abstract: Transformer-based language models for SMILES strings suffer from a locality gap: standard character-level tokenization fragments chemically meaningful motifs, forcing models to repeatedly learn local syntax at the expense of long-range dependencies.
The study investigates how document segmentation and chunk representation affect retrieval-augmented generation (RAG) for chemistry texts. Using the ChemQuests corpus, the authors benchmark 41 embedding models and evaluate them across five chunking strategies, seven chunk sizes, and various overlap settings. They find that embedding choice has the largest impact, with models like E5, BGE, and Nomic performing best, and recommend medium-to-large chunks with fixed-token, recursive-token, or hierarchical-section chunking and low overlap for effective chemistry-aware RAG.
Large language models (LLMs) are widely applied across chemical tasks, such as molecular property prediction, which underpins drug discovery. Molecular LLMs represent a molecule through several modalities, notably a 1D SMILES sequence or a 2D molecular graph.
arXiv:2609.06898v1 Announce Type: cross Abstract: Byte Pair Encoding (BPE) constructs vocabularies through greedy pair merging, but the resulting merge order does not necessarily allocate a fixed mod...
arXiv:2607. 23319v1 Announce Type: cross Abstract: Standard subword tokenization algorithms such as Byte-Pair Encoding (BPE) and SentencePiece are trained predominantly on modern language corpora and produce inefficient segmentations when applied to classical Indian languages.
arXiv:2606. 05693v1 Announce Type: new Abstract: Large language models (LLMs) have shown promise for molecular property prediction, but their ability to reason over chemical structures remains limited, as molecular representations such as SMILES differ substantially from the natural language on which LLMs are primarily trained.
arXiv:2608. 10480v1 Announce Type: new Abstract: Large language models (LLMs) are widely applied across chemical tasks, such as molecular property prediction, which underpins drug discovery.
arXiv:2609.15991v1 Announce Type: new Abstract: Standard subword tokenizers either treat every orthographic variation of a word (such as hello, Hello, HELLO, and H\'ello) as unrelated vocabulary entr...